MolNFT v1 · #50092 · protein

Crystal structure analysis of human synaptotagmin 1 C2A-C2B

2R83 · Synaptotagmin-1: “Crystal structure analysis of human synaptotagmin 1 C2A-C2B”. X-ray diffraction, 1 ligand (CL), 5 pockets (best druggability 0.81). MolNFT v1 #50092 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2R83
Type: protein
Length: 558 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Synaptotagmin-1
UniProt: P21579
Ligands: CL
Pockets: 5 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Synaptotagmin-1	protein	279	10% helix, 46% strand	P21579

Ligands and binding sites

CL · Chloride ion · ion · 8 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1061	0.81	0.82	128	CL
2	107	0.58	0.85	28	CL
3	93	0.55	0.85	24	CL
4	58	0.32	0.76	9	empty
5	60	0.29	0.75	16	empty

Interfaces

1 interface between chains.

A–B · 1131 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

2R83 · Crystal structure analysis of human synaptotagmin 1 C2A-C2B · the same entry in another collection · chain A against A, TM-score 1.00
P21579 · AlphaFold monomer V2.0 prediction for synaptotagmin-1 (P21579) · a predicted model of the same protein · chain A against A, TM-score 0.55

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P21579
Elsewhere: RCSB PDB 2R83 · PDBe 2R83 · UniProt P21579

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